CNVDetectionResult-class
                        Class "CNVDetectionResult"
CNVRanges               Genomic locations and indices of the simulated
                        CNVs.
X                       A simulated data set for CNV detection from NGS
                        data.
XRanges                 A simulated data set for CNV detection from NGS
                        data.
cn.mops                 Performs the cn.mops algorithm for copy number
                        detection in NGS data.
cnvr                    These generic function returns CNV regions of a
                        CNV detection method stored in an instance of
                        'CNVDetectionResult-class'.
cnvs                    These generic function returns CNVs of a CNV
                        detection method stored in an instance of
                        'CNVDetectionResult-class'.
getReadCountsFromBAM    Generates the read counts from BAM Files. These
                        counts are necessary for CNV detection methods
                        based on depth of coverage information. Note
                        that the function is much faster, if the BAM
                        files have an index file. The index file is
                        assumed to be in the same folder and have an
                        identical file name except that ".bai" is
                        appended.
getSegmentReadCountsFromBAM
                        Generates the read counts from BAM Files for
                        predefined segments. This is the appropiate
                        choice for exome sequencing data, where the
                        bait regions, target regions or exons are the
                        predefined segments. These counts are necessary
                        for CNV detection methods based on depth of
                        coverage information. Note that the function is
                        much faster, if the BAM files have an index
                        file. The index file is assumed to be in the
                        same folder and have an identical file name
                        except that ".bai" is appended.
haplocn.mops            Performs the cn.mops algorithm for copy number
                        detection in NGS data adjusted to haploid
                        genomes. It is assumed that the normal state is
                        copy number 1. This is an experimental method
                        at the moment.
individualCall          These generic function returns the individual
                        calls of a CNV detection method stored in an
                        instance of 'CNVDetectionResult-class'.
iniCall                 These generic function returns the
                        informative/non-informative call of a CNV
                        detection method stored in an instance of
                        'CNVDetectionResult-class'.  The I/NI call is a
                        measure for a genomic segment across all
                        samples, whether this segment is a CNV region
                        (informative) or a normal genomic region
                        (non-informative).
integerCopyNumber       These generic function returns the integer copy
                        numbers of a CNV detection method stored in an
                        instance of 'CNVDetectionResult-class'.
localAssessments        These generic function returns the local
                        assessments, i.e. signed individual
                        informative/non-informative calls, of a CNV
                        detection method stored in an instance of
                        'CNVDetectionResult-class'. For other CNV
                        detection methods this can be (log-) ratios or
                        z-scores.
normalizeChromosomes    Normalize quantitative NGS data in order to
                        make counts comparable over samples. Scales
                        each samples' reads such that the coverage is
                        even for all samples after normalization.
normalizeGenome         Normalize quantitative NGS data in order to
                        make counts comparable over samples. Scales
                        each samples' reads such that the coverage is
                        even for all samples after normalization.
normalizedData          These generic function returns the normalized
                        data of a CNV detection method stored in an
                        instance of 'CNVDetectionResult-class'.
params                  These generic function returns the parameters
                        of a CNV detection method stored in an instance
                        of 'CNVDetectionResult-class'.
plot-methods            Plots a CNVDetectionResult
posteriorProbs          These generic function returns the posterior
                        probabilities of a CNV detection method stored
                        in an instance of 'CNVDetectionResult-class'.
                        The posterior probabilities are represented as
                        a three dimensional array, where the three
                        dimensions are segment, copy number and
                        individual.
segment                 Performs a fast segmentation algorithm based on
                        the cyber t test and the t statistics.
segmentation            These generic function returns segmentation of
                        a CNV detection method stored in an instance of
                        'CNVDetectionResult-class'.
segplot                 Plots the log normalized read counts and the
                        detected segments for one sample on one
                        reference sequence.
show-methods            Displays the result object of a copy number
                        detection method.
